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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Interaction pattern similarity measured by Grim
You can zoom onto the graph by using the mouse to make a selection

Binding Modes are compared using Grim.
For more information, please see the following publication: Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65


Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
4htf SAM tRNA 5-carboxymethoxyuridine methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.890
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.778
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.727
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.718
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.717
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.714
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.710
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.708
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.708
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.706
5bxy SAHPutative RNA methylase family UPF0020 / 0.705
3lcc SAHThiocyanate methyltransferase 1 / 0.703
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.698
1jqd SAHHistamine N-methyltransferase 2.1.1.8 0.697
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.695
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.692
5bp7 SAHSAM-dependent methyltransferase / 0.692
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.691
2yqz SAMUncharacterized protein / 0.690
3ou2 SAHSAM-dependent methyltransferase / 0.689
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.688
3kkz SAMUncharacterized protein / 0.687
3t7s SAMUncharacterized protein / 0.687
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.687
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.686
3t7t SAHUncharacterized protein / 0.686
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.686
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.685
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.683
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.682
3fri SAH16S rRNA methylase / 0.679
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.678
4e2x SAHMethyltransferase / 0.678
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.678
2p35 SAHTrans-aconitate 2-methyltransferase / 0.677
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.676
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.676
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.675
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.675
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.674
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.674
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.674
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.674
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.673
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.672
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.672
2zfu SAHRibosomal RNA-processing protein 8 / 0.671
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.670
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.669
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.669
2jib ADPOxalyl-CoA decarboxylase 4.1.1.8 0.669
3duw SAHO-methyltransferase, putative / 0.669
3go4 SAHUncharacterized protein / 0.669
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.668
3sxj SAMPutative methyltransferase / 0.668
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.667
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.666
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.666
4c04 SFGProtein arginine N-methyltransferase 6 / 0.665
5epe SAHUncharacterized protein / 0.665
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.664
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.664
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.664
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.662
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.662
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.662
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.662
2o06 MTASpermidine synthase 2.5.1.16 0.661
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.661
3e8s SAHUncharacterized protein / 0.661
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.661
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.660
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.660
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.659
2pan FADGlyoxylate carboligase 4.1.1.47 0.658
4nec SAHPutative SAM-dependent methyltransferase / 0.658
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.657
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.657
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.657
3p9c SAHCaffeic acid O-methyltransferase / 0.656
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.655
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.654
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.654
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.654
4qpp SAHProtein arginine N-methyltransferase 6 / 0.654
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.653
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.652
1g38 NEAModification methylase TaqI 2.1.1.72 0.651
3e23 SAMUncharacterized protein / 0.651
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.651
3qgz ADNHistidine triad nucleotide-binding protein 1 3 0.650
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.650